Revert "Added optimisation to nvcc in cmakelists"

This reverts commit e918db17a037e60ebf3eb23d6e9c28eafb4ac62e.
Revert "Revert "Moved to constructing ell from the outset in the hope of better performance""

This reverts commit 4c4d8aea298c63ade692063a41ac01112c472b41.
Revert "Moved to constructing ell from the outset in the hope of better performance"

This reverts commit 49cd864d4b79dc16e0834854fd672443f73f1a56.
Revert "Trying out csr matrix to check speed"

This reverts commit e8a24f5b42940d18f65e5a1c8cb497138d246912.
Added nvcc compiler optimization
Moved to using diagonal preconditioner in cuda solvers
Added nUpdates argument to thermalize function to allow some more flexibility
Implemented warmup updates in python simulation and xml input files
Merge branch 'master' of ssh://orentago.linkpc.net:535/pyQCD
Removed completed items from todo list